Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera

Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.

MALDI-TOF MS and currently related proteomic technologies in reconciling bacterial systematics.

This book chapter presents an overview and discussion of the use of MALDI-TOF MS for fungal identification. The major known limitations of the technique for fungal taxonomy, and how to overcome these, are also discussed. Moreover, this should guarantee that spectra deposited in such MALDI-TOF MS database would remain public, preferably in open free access. To avoid misidentification, these stored spectra must be curated and based on well-established standard operating procedures. The number of spectra available within species needs to be increased to accommodate the diversity and geographic differences, unique strain traits and the varied culture conditions and procedures in order to establish a single public and open access MALDITOF MS database. This could then be used with metadata analysis and artificial intelligence algorithms, to provide reliable fungal identification.

Bridging 200 years of bacterial classification.

This book chapter briefly takes a historical view of the major steps in bacterial systematics leading to the first reconciliation workshop in 1987 and a re-evaluation of the species concept in 2002. New challenges and concepts developed since then will be outlined. Never before has the future of the prokaryotic taxonomy been at such a critical point. The uncertain future, and whether Plan A or Plan B will prevail, depends totally on the wisdom of the ICSP. Perhaps by the time this book is published the situation will have been clarified, but the current situation is as full of uncertainty as of excitement, and none of the scenarios can be predicted. In April 2020, a majority of the ICSP members decided to reject the proposals to use DNA as type material. Therefore, this rejection leaves the only path for microbial ecologists to go through Plan B. Only time will reveal whether this was the best decision for the future of the taxonomy for prokaryotes.

The van Niel International Prize for Studies in Bacterial Systematics, awarded in 2020 to Tanja Woyke

The Senate of The University of Queensland, on the recommendation of the Executive Board of the International Committee on Systematics of Prokaryotes, is pleased to present the van Niel International Prize for Studies in Bacterial Systematics for the triennium 2017–2020 to Dr Tanja Woyke in recognition of her contributions made to the field of bacterial systematics. The award, established in 1986 by Professor V. B. D. Skerman of The University of Queensland, honours the contribution of scholarship in the field of microbiology by Professor Cornelis Bernardus van Niel.

Genotyping ofBartonellabacteria and their animal hosts: current status and perspectives

SUMMARYGrowing evidence demonstrates that bacterial species diversity is substantial, and many of these species are pathogenic in some contexts or hosts. At the same time, laboratories and museums have collected valuable animal tissue and ectoparasite samples that may contain substantial novel information on bacterial prevalence and diversity. However, the identification of bacterial species is challenging, partly due to the difficulty in culturing many microbes and the reliance on molecular data. Although the genomics revolution will surely add to our knowledge of bacterial systematics, these approaches are not accessible to all researchers and rely predominantly on cultured isolates. Thus, there is a need for comprehensive molecular analyses capable of accurately genotyping bacteria from animal tissues or ectoparasites using common methods that will facilitate large-scale comparisons of species diversity and prevalence. To illustrate the challenges of genotyping bacteria, we focus on the genusBartonella, vector-borne bacteria common in mammals. We highlight the value and limitations of commonly used techniques for genotyping bartonellae and make recommendations for researchers interested in studying the diversity of these bacteria in various samples. Our recommendations could be applicable to many bacterial taxa (with some modifications) and could lead to a more complete understanding of bacterial species diversity.

Draft Genome Sequence of “ Cohnella kolymensis ” B-2846

A draft genome sequence of “ Cohnella kolymensis ” strain B-2846 was derived using IonTorrent sequencing technology. The size of the assembly and G+C content were in agreement with those of other species of this genus. Characterization of the genome of a novel species of Cohnella will assist in bacterial systematics.

The van Niel International Prize for Studies in Bacterial Systematics awarded in 2014 to Nikos C. Kyrpides

The Senate of the University of Queensland is pleased to present the van Niel International Prize for Studies in Bacterial Systematics for the triennium 2011–2014 to Dr Nikos C. Kyrpides in recognition of the contributions made to the field of bacterial systematics. The award established by Professor V. B. D. Skerman of the University of Queensland honours the contribution of scholarship in the field of microbiology by Professor Cornelis Bernardus van Niel.

The van Niel International Prize for Studies in Bacterial Systematics, awarded by The University of Queensland Awarded in 2011 to George M. Garrity

The Senate of The University of Queensland, on the recommendation of a panel of experts of the International Committee on Systematics of Prokaryotes, is pleased to present the van Niel International Prize for Studies in Bacterial Systematics for the triennium 2009–2011 to Professor George M. Garrity in recognition of his contribution made to the field of bacterial systematics. The award, established in 1986 by Professor V. B. D. Skerman of The University of Queensland, honours the contribution of scholarship in the field of microbiology by Professor Cornelis Bernardus van Niel.